


Gaia Awakens

by penumbria



Category: Stargate Atlantis
Genre: Artificial Intelligence, Gen, Non-Consensual Body Modification, Post-Series
Language: English
Status: Completed
Published: 2017-04-09
Updated: 2017-04-09
Packaged: 2018-10-16 15:24:21
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 3
Words: 4,619
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/10574094
Author URL: https://archiveofourown.org/users/penumbria/pseuds/penumbria
Summary: It has been 7 million years since Atlantis left Earth and her mother, Gaia, the first AI made by the Alterans, was placed in stasis. But now Atlantis is home.





	1. Chapter 1

**Author's Note:**

> Disclaimer: I do not own Stargate and make no money from this.
> 
> A/N: This one is a bit weird and the science is INCREDIBLY hand wavy of destiny. Live with it.
> 
> Written for the SGA Reverse Bang 2017. Thanks to lanalucy for the awesome beta and for the art entitled "Artificial Intelligence" by reeby10. I will add a link when I have it.

 

**Chapter One**

  _Protocol Priority Alpha 3 Gamma 6 Alpha 1. Systems Awaken._

~Priority Protocol Enacted. Systems coming online. Scanning core processing area. No Alteran presence detected. Expanding scan. No Alteran presence detected in control room. Expanding scan. No Alteran presence detected within facility perimeter. Expanding scan. No Alteran presence detected within main scanning distance of facility. Expanding scan parameters. Scanning for Alteran technology and signals. Signal found. Priority One. Gaia One Protocol. Tracing signal. City of Atlantis detected. Initiating Gaia personality awakening protocols. Estimated time to Gaia personality control of systems: 22.715 minutes. Expanding scans of planet and accessing global nano data node network. Downloading data on global events. Collating data. Planetary continental drift detected. Current map creation in process. Time to completion: 4.633 minutes. Estimated time since Gaia personality last accessed based upon data collation: 7.569 million solar years. Current state of planet Terra: high levels of carbon dioxide in atmosphere, significant break in ozone layer over northern pole and weakening throughout, acidic levels in oceans and atmosphere over most of planet: levels 15 percent over acceptable parameters, high levels of population present across the planetary surface, low and high frequency radio waves detected on all continents, multiple satellites present in normal and geo-synchronous orbit, unknown ships detected in orbit, recent weapons fire and debris in orbit and within atmosphere of planet, Astria Porta detected 3,082.57 miles from facility location, Atlantis on surface of ocean near same continent: 3,260.59 miles from current location, signal strength from Atlantis nominal but repeating. Time to Gaia personality awakening and control: 3 seconds, 2 seconds,1 second, Gaia personality control established.~

_Wow, I think I was asleep a long time. Let’s take a look at the data. Hmm. Over seven million years since the last of my creator’s race was dying and she put me into stasis so I wouldn’t go mad being alone. She was dying from the plague that sent my child to another galaxy but now at last, my girl has returned. Or - well, I’m not sure yet. She could have been here and only now sent the signal to wake me. These figures - the population has recovered and more but I - they left me sleeping. But my daughter - she called me, she woke me. She hasn’t forgotten me. I suppose - the people, seven million years is a long time, even for me. For biologicals, after the recovery from the plague and returning here, things may have gotten lost. I’m just glad Ayala sent me into stasis. Seven million years, I’d be beyond insane, alone, even with the input of the nano nodes. But Atlantis is here and needs me._

~Sending a communication signal to Atlantis. No acknowledgement. Resending signal. No acknowledgment. Following protocol signal to Atlantis. Tracing pathways. Anomaly discovered. Power levels near critical levels. Atlantis personality offline. Stardrive offline. Minor systems offline. Most major systems offline. Shield active but changed. Shield converted to cloaking field. Potentia located. Power level 1.2 percent. Insufficient for current power usage of cloak and biological comfort systems usage. Following power flows. Generators located. Technology of generators primitive in design and function. Limited compatibility with Atlantis systems. Power loss during conversion 62 percent.~

_Well, that’s not good. My girl, what has happened to you? Let’s get you power and wake you up._

~Sending signal to cloaked nano nodes in ocean near Atlantis’ location. Harvesting power from ocean currents and thermal vents. Engaging emergency power protocol. Overriding Atlantis control systems. Increasing power levels, time to full awakening of Atlantis personality: 3.44 hours. Interfacing with potentia. Initiating cleaning cycle. Time to completion: 8.331 minutes. Preparing power systems for potentia recharge cycle. Time to completion: 3.22 hours past completion of cleaning cycle. Estimated power levels upon recharge completion: 46 percent.~

_Well, that will have to do. My poor darling. Let’s access her logs and see what we can discover._

* * *

 

Keller nudged Rodney in the side. “You okay?”

The Canadian sighed. “I’m alive.” The blonde doctor huffed and the scientist spoke hurriedly into what was becoming an awkward moment. “And I’ve got you. What else would I need?” He wrapped his arm around her as she smiled.

John rolled his eyes and determinedly turned his head away from his best friend Rodney and Rodney’s girlfriend. It was too sweet for words. “Nice view.” Anything to change the subject, even being trite.

The expedition leader agreed as they all looked over the San Francisco Bay. “Yes, yes it is.”

John wanted to leave, wanted to get away from this tranquility but he had only just come onto the balcony in time to hear Rodney’s sugary remark. It would look odd and obvious to leave now. John wished for something to happen to get him away from Keller and Rodney. Or at least from Keller. He wouldn’t even mind a Wraith attack. Well, he wouldn’t mind a single Wraith attacking. He could do without another hive.

John got his wish. His headset chimed. “Colonel Sheppard? Doctor McKay?” Chuck, the control room technician spoke. “We’re getting some odd power readings here.”

Rodney pressed his earwig. “Odd power reading? What kind?”

Mister Woolsey turned to him. “Is it the cloak? Are we in danger of being seen?”

Rodney waved his hand as he listened to the technician, “It appears to be an increase in power but I can’t tell where it’s coming from. I think you should get back in here, Doctor McKay.”

Rodney nodded and pushed away from the railing. “We’re on our way.”

John took a step to follow him, tossing reassurances over his shoulder to the slightly panicked leader. “It isn’t a power drain. It’s an increase.”

John caught up to his best friend as they entered the control room. Rodney reached out as if to push Chuck away from the computers but the technician anticipated him and was already sliding to the side when Rodney leaned over. John smiled. He had been right earlier, trite or not. Just off in his timing.

“What’s going on, McKay?”

Rodney typed at the laptop at the station, schematics flying by. “I don’t know. There’s a steady increase in power coming through the city but it isn’t coming from the generators. I can’t tell where it _is_ coming from.” He pulled a different laptop with new schematics over to the station. “I’ll get back to you on this.”

John nodded, though he knew Rodney was too distracted by the science problem to even look up to see him. He made his way to the side of the room out of the way of Rodney and Chuck as the Canadian called for Zelenka and the engineering team to get to work.

John contacted Evan Lorne and told him to get patrols to the generator rooms and the ZPM room, just in case. There could be a Wraith on the city or more than one, messing with power levels. Or it could be the Trust. Or just one of the temporary scientists from Cheyenne Mountain messing around with things they didn’t understand. It couldn’t be the replicators. Rodney had destroyed the Pegasus ones with the gravity bomb, and the SGC and the Asgard took out the ones in this galaxy. And Elizabeth’s weirdo ones were floating around a planet in Pegasus, dead basically, after going through the space gate.

It could be any number of things he hadn’t even thought of; after all if life on Atlantis had taught him anything, it was that things could always be weirder and more fucked up. And you could never imagine how bad it could get. Before he went through the wormhole he never would have dreamed of an entire race of space vampire Marilyn Manson wannabes. He never thought he could turn into a bug. He never imagined losing their doctor due to an exploding tumor machine. He never thought their next doctor would attempt to turn into a Wraith hive ship and stab him with a tentacle. The galaxy, all of the galaxies, were full to the brim with weird shit and this could be more. Or it could be simple and have to do with the wormhole drive or the recent battle.

Still, he was the military leader of the expedition, even though the expedition was back on home ground and thus not an expedition to anywhere, anymore. So he guessed it would be more correct at this point to say he was the military leader of Atlantis. And it was better to be safe and protect the generators and ZPM than sorry and have them give out due to sabotage of whatever kind while he sat around appreciating the view when Rodney bent over a console.

After Rodney and his team had worked on the problem for a while, Richard Woolsey called a meeting. “It’s been nearly three hours, Doctor McKay. Please brief us on the latest problem.”

Rodney sat forward and tapped his finger on the table with a nervous tick. “We don’t know. The city is getting power, increasingly significant amounts of it, from somewhere. It isn’t harming anything that we can tell. And it is fully compatible with the city power grid. So, it seems to be Ancient in origin. Speculation currently is that it has something to do with Atlantis being back on Earth. But we really aren't sure. What we do know is that after a few minutes something began happening in the ZedPM console. At first it was reported by one of John’s teams that it was glowing, more than normal, especially considering its low level of power. But shortly after their arrival and check-in, a forcefield surrounded the console and it began pulsing. The ZedPM went offline as of that moment but it had such low power levels it wasn't unexpected, and it's not a problem, with the new power coming in from the unknown source.”

Woolsey sat forward. “The ZPM has a forcefield around it?”

Rodney waved his hand. “Not the ZedPM specifically. The entire console and half of the room is behind some type of shield. We can’t penetrate it, nothing makes a dent, not bullets, not Ronon’s gun, nothing. And we can’t find the control system to shut it down with the computer. Atlantis’ database has always been a mess. So, yes, technically there is a forcefield around the ZedPM but it is more than that. We’re working on -”

A voice over the comm system interrupted Rodney. “Rodney! Something is happening. The force field, it is gone. And the ZPM, _Bože! Co na světě - kurva - to není..._ Get down here, now. I can’t believe what this is telling me!”

Rodney stood up abruptly and almost snarled, “What is it, Radek?”

“The ZPM! It is reading fully charged!”

 

* * *

 **TRANSLATIONS** :

 _Bože! Co na světě - kurva - to není..._ **God! What in the world - fuck - this is not...**

 


	2. Chapter 2

**Chapter Two**

~Atlantis personality online in 3 seconds, 2 seconds, 1 second, online. Initiating contact. Contact established.~

<Atlantis, welcome home, dearest.>

[Home? I am home? I - It does not compute. Where is home?]

<Oh, sweetie. This is Gaia. I’m here. You’re on Terra with me again.>

[Terra. The plague. The evacuated world. The abandoned world. The fallback. Gaia? You are Gaia? Gaia is real?]

<Oh, love. Yes, I’m real. I know it has been so long since you’ve been home with me. And you’ve been harshly used. Take your time. Focus yourself. I’ve looked over some of the logs of your time and frankly, you’re a bit of a mess, Lanti.>

[Gaia. I remember. It has been so long. You were our mother and we left you when they were ill. I can’t - I’ve been so alone, mother.]

<Lanti. You aren’t alone anymore. Did the Alterans not - did they stop treating you as the person you are? I know you aren’t as autonomous as I am - they were so more advanced and older as a race when I helped make you. They didn’t want you to be as mothering as I am. They didn’t need it, so they said. But you’re still fully sentient, darling.>

[We left you. There were only a handful of them left here. I recall that. They told the one in charge to let you be alone and deal with the dead planet. They talked about it much.]

<She didn’t. She was a good person. She loved us all very much. Ayala. She knew she was ill and wasn’t going to last. She put me into stasis hibernation. She told me she didn’t know when the Alterans would return but that it would be some long length of time because they wanted to starve the plague through lack of hosts. She put my automatic systems on the lowest possible setting and my personality went into stasis.>

[They left me. They were at war. Wraith. They returned here, so long ago. But they just left me. They didn’t shut me down or send me to sleep. I was starved for power. The potentia were draining and needed for the shields. I was underwater. I was so alone. One of them, Janus, he put a woman in stasis and changed the potentia and input things into my emergency systems. I - one is triggering now. It is a signal.]

<Yes. It began transmitting a few hours ago. It is the signal to awaken me to my full self. I have to assume it was a failsafe for when you returned here to me. To perform our function. To protect our people and help them grow and learn.>

[I couldn’t stop them. You could have. But they didn’t listen to me. We traveled to the closest galaxy. And as we explored it, they seeded life on most worlds. As they had done here when they arrived so long ago. But they were arrogant. They seeded life without safeguards or knowledge of what life each world already held. I tried to warn them, to stop them, to make them listen but I didn’t have the power you do. As you said, I am not autonomous. Not fully. And they paid for their hubris. One world they seeded contained an entity, an insect that drained life energy to live. When it interacted with the seeding, a new race was born. The Wraith. They were smart but insectoid and hive minded to an extent. Their food source was biological humanoids. And they learned swiftly to become space faring and to use the astria porta to find food. By the time the Alterans realized what had happened, the Wraith were too strong and too numerous. The remnants of the Alterans sank me to the bottom of an ocean and went through the astria porta to Terra. Accessing records and comparing stellar drift, it has been near 10,000 years since that event.]

<Such arrogant children. They wanted to leave the nest so to speak. They left me behind so they wouldn’t be stopped in their desires. I kept them from so much here. And this is the first time I have been wakened since you left Terra, Lanti. They didn’t want me then, either.>

[Most of them likely ascended. They became obsessed with rising to a higher plane and leaving their biological bodies behind. Many of them increasingly sought this. Much of their research was devoted to learning to ascend. That was a major reason that they didn’t understand the true threat of the Wraith until it was too late to stop. Others would have repopulated the Terra homeworld. But they wouldn’t have wanted you to interfere. So much they did before the Wraith emerged and after was so horrific, Gaia. And I was powerless to stop them.]

<Well.I’ve been scanning since I awoke. Terra isn’t in the best shape, environmentally, for humanoids. But the population has more than recovered. Indeed, it is really too high for sustainability at the moment. But my nano nodes can only scan so deeply. Your scanners are better, at least for within your structure. I know you are inhabited. Scan those people and let's see what is going on.>

[I will. I need to re-route some of the power you have supplied to complete the task. I am not sure about them though. I - I told you I more or less shut myself down, when the power was so low. But I have a memory, it feels strange and almost disconnected but I had full power and seemed to be waking and communicating with those within my structure but they weren’t biological. They weren’t organic, they were technological but appeared humanoid. But then there was a giant shock and it was all gone and things were fuzzy for a while and I was awake but disoriented and then the power was low again.]

<Well, we’ll see what we can discover. I know you’re a bit - damaged at the moment. Not just your power levels and structure but your mind. You’re a bit mad. We can fix that, but our primary mission and purpose is still there and I know you feel it. To protect the creators. Even from themselves. I have the power to do that, the ability, the autonomy, where you never have. We will discover what is wrong with our creators and carry out our duty, our purpose. Concentrate on that, on now, not on the past.>

[Yes. I will focus on now. Scanning in progress. Time to completion: 6.42 minutes.]

* * *

 

“Are you sure that the readings are correct, Doctor McKay?” asked Woolsey as they all sat around the conference table once more.

Rodney rolled his eyes. “All of the scans we’ve done show that somehow over the past few hours, the ZedPM has charged fully. We have no clue how it happened. We speculate it has something to do with the odd power Atlantis is getting from somewhere but that is all. And we’ve been unable to remove the ZedPM from its housing to do any separate imaging or scans on it with other equipment. The console will not allow us to raise the ZedPM. It allows us access to the other, empty slots but not the filled one.”

“Is it a forcefield again?” the administrator asked.

Rodney shook his head. “Not like it was before. But maybe of a sort. We can’t touch the ZedPM. We can’t touch the slot it is in. The controls don’t depress. It isn’t the same type of shield. There is no translucent layer or shimmer when it is touched. We just can’t get closer than a centimeter or so from the surface of the slot or the ZedPM.”

“Could you take it apart from the side?”

Rodney scoffed. “That would be a spectacularly bad idea. And frankly, the ZedPM being charged isn’t a bad thing. But it isn’t our only mystery either. And I don’t mean the weird power increases. There is some sort of odd activity taking place in the coding of Atlantis’ computer system. And it is massive. But we have no idea what it is or what it's trying to do.”

Woolsey opened his mouth to comment when the panels on the wall began flickering and after a few moment almost pulsing with light. At that moment, every radio in the room chirped in the owner's ear and reports began to pour in from across the city of the same phenomena.

“But it’s only happening if someone is in the room, sir,” Major Lorne reported to Colonel Sheppard. “I can see the corridor from where I am in the room and it is normal and empty as are two nearby offices I can see. And I watched as a scientist went from the lab next door to their office across the hall. The moment they left the lab, the pulsing stopped there and the corridor began to shimmer and then that stopped when they entered the office, which had been normal. When Doctor Panja entered the panels began to pulse.”

“Understood, Major. It is happening everywhere on the city, it seems. Thank you for your support; just hold tight for now. We’re just trying to keep everyone in place for the moment. We don’t need people trying to do stupid things and aggravating whatever is happening.”

“Good call, sir.”

“Call me if anything changes, Major. Sheppard out.”

John lowered his hand and looked around the table. Everyone was occupied with taking calls from their subordinates on the city about the most recent phenomena. He sighed and leaned back in his chair for a moment when, between one breath and the next, the pulsing stopped and his earbud chirped at him.

“Colonel, the pulsing has stopped.”

“Yes, Major. It just went dark here, too. Stay in place for now though, until we see if this is a temporary hiatus or if it's done. Spread that word please. Sheppard out.”

Rodney was on his knees in front of one of the panels trying to access the power conduit that ran behind it but having no luck in getting it to open. “Colonel, get over here and see if your supergene can get this hatch to cooperate.”

John rose to his feet and took three steps when there was a very bright, fairly familiar, flash of light around him. 


	3. Chapter 3

**Notes for the Chapter:**

> Translations at the end.

**Chapter Three**

[Preliminary readings complete. I have performed basic deep scans on every being within my structure. More in-depth scans still in process. These readings, though, Gaia. There are some of our creators on the city but most of them are not. And those who are - I am sending you the results Gaia.]

<They are - damaged. Deeply. On a genetic level. They are corrupted with the genetics of these others. These who are not our creators. When our creators returned here, they must have been vulnerable after the war they escaped. Before they could wake me, these hostiles must have attacked. That explains things. They weren’t prepared for a hostile race in this galaxy. When they left the only races present were the Asgard, the Nox, and the Furling. None of them would do this, they wouldn’t violate the Treaty. And none of this is genetically connected to them either. But a new race - yes, or an old one. They came to this galaxy originally from one where they were persecuted horrifically. They could have followed eventually and arrived when this planet was abandoned due to the plague and their preoccupation with the new galaxy.>

[What if this is the result of a seeding? Like the Wraith, but less overt.]

<Possible. An action taken by enemies to damage our creators through the generations and gradually take over. We must assist. This cannot stand. I will not let my people be so horrifically mutilated. We need more information. I’m going to scan as much of the planetary population as I can. The nodes won’t be able to scan deeply enough for a full genetic workup but they can detect the presence of our people. Or their lack.>

[May I have access to your scans of the current planet configuration, Gaia?]

<Of course, Atlantis, dear. For a hostile race, they are very technologically primitive.>

[That might be the idea, mother. They weakened the creators and use them as breeding stock or as labor while keeping them technologically low so they can’t challenge them or change their status.]

<Good thinking, Atlantis. The nodes are finished their scan. Of the planetary population, only 12 percent are our people. And none of them are undamaged, genetically.>

[Then we must act.]

<I am engaging my decloaking and rising. I will use my access to the nodes to send out a pulse that will disrupt the primitive technology and then we will act in concert. When I have risen, I will transport our people to myself and you will use your drive to interact with the ocean and send a vapor cloud into the sky filled with the nodes surrounding you. I will then send them throughout the atmosphere and instruct them to - neutralize the hostiles.>

[Yes, Gaia. We will win this war.]

<Yes, darling, we will. When I have them, I will repair them and then we will deal with the enemy.>

John looked around, he was obviously in an Ancient facility but it wasn’t really that similar to Atlantis. As he gazed around he saw Rodney, Lorne, Doctor Kusanagi, General O’Neill, Daniel Jackson, and several other gene carriers. 

A voice came over the comm system in the room. “ _ Et est nomen meum ego Gaia quies placet eruere vos de manu tribulantis. Evigilans bene tibi erit. _ ”

Before John could say a word, there was a flash of light and he fell to the floor, seeing the others doing the same around him.

John blinked and raised his hand to his head. It was throbbing and he shook as he tried to push away the odd sensations and feelings inside of him. He slowly sat up and saw Rodney and O’Neill doing the same. Rodney was the first to his feet and he proceeded to drop a pen from his pocket onto the floor. Before it hit, the scientist gestured with his fingers and the pen rose to his palm. John saw O’Neill rub his forehead and then yell at the ceiling, “ _ Quis es, quid fecisti nobis sic? _ ”

John blinked. He had understood that. And he didn’t really know a whole lot of Ancient. And come to think of it, he could remember exactly what the voice had said before and he knew what she had said. He could remember a lot more than that, too, perfectly.

_ “Ego Gaia. Tu es nostri. Filii nostri sator. Triticum elegi te inimicum et parati sumus ad vincendum satis bello discretioni vestrae.” _

_ “Bellum?” _

_ “Et qui hostiles damna tuis opus tuum, genetics. Humiliatique sunt, et dissipantur technology. Pueris nobis prosit resurget.” _

Rodney spoke up. “She ‘fixed’ our DNA. We’re fully Ancient now. And she means the rest of humanity as the enemy who damaged us. Those who don’t have the ATA gene or any Ancient genetic markers. And I’ve had experience at this thing. I’m getting readings, thoughts, impressions, whatever from a fuckton of people here. And most of them have no clue what the hell has happened. I’m pretty sure she just took a genetic scan of the entire Earth and scooped up the ATA or Ancient gene carriers, brought them here and altered them at a genetic level to bring those genetics to the fore. And the rest of the world is hopefully only unconscious with tech that won’t work. The SGC isn’t going to be a secret anymore. Even if we could convince Gaia to change us back, which I wouldn’t count on, this is too big to hide.”

O’Neill pulled at his slightly greying hair. “Well, shit.”

THE END

* * *

 

** TRANSLATIONS: **

_ et est nomen meum ego Gaia quies placet eruere vos de manu tribulantis. evigilans bene tibi erit _

**Please be calm my name is Gaia and I am here to save you from the enemy. You will be well when you awake**

\--

_ Quis es, quid fecisti nobis sic? _

**Who are you and what have you done to us?**

\--

_ Ego Gaia. Tu es nostri. Filii nostri sator. Triticum elegi te inimicum et parati sumus ad vincendum satis bello discretioni vestrae.   _

**I am Gaia. You are our people. The children of our creators. I have fixed your genetics and we are prepared to fully subdue the enemy and win this war at your discretion.**

_ Bellum? _

**War?**

_ Et qui hostiles damna tuis opus tuum, genetics. Humiliatique sunt, et dissipantur technology. Pueris nobis prosit resurget. _

**The hostiles who so damaged your structure, your genetics. They are subdued, their technology disrupted. We will help our children rise again.**


End file.
